Starting phenix.real_space_refine on Tue Aug 26 10:14:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xme_38473/08_2025/8xme_38473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xme_38473/08_2025/8xme_38473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xme_38473/08_2025/8xme_38473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xme_38473/08_2025/8xme_38473.map" model { file = "/net/cci-nas-00/data/ceres_data/8xme_38473/08_2025/8xme_38473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xme_38473/08_2025/8xme_38473.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 218 5.16 5 C 22444 2.51 5 N 6235 2.21 5 O 6593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35567 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 8665 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 454 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 27, 'ASN:plan1': 8, 'ASP:plan': 27, 'ARG:plan': 11, 'PHE:plan': 5, 'GLN:plan1': 8, 'TYR:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 359 Chain: "B" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8053 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1020} Chain breaks: 9 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 35, 'ASP:plan': 22, 'GLN:plan1': 5, 'TYR:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 265 Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2111 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 14, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 866 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1505 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "F" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1096 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 9, 'TRANS': 164} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 8, 'GLU:plan': 9, 'ARG:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 830 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 715 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "L" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8019 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 40, 'TRANS': 1011} Chain breaks: 3 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 12, 'ASN:plan1': 5, 'GLN:plan1': 8, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 283 Chain: "N" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 563 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 2 Chain: "O" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 223 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "Q" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 602 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 334 SG CYS A 56 49.144 66.364 119.602 1.00220.62 S ATOM 352 SG CYS A 59 49.666 70.524 120.492 1.00227.99 S ATOM 399 SG CYS A 67 50.619 68.946 116.914 1.00205.33 S ATOM 6988 SG CYS A1031 145.376 70.292 84.541 1.00203.71 S ATOM 7057 SG CYS A1044 142.969 71.660 87.299 1.00167.74 S ATOM 625 SG CYS A 97 100.309 62.720 139.893 1.00314.29 S ATOM 642 SG CYS A 100 100.133 63.141 143.790 1.00300.94 S ATOM 673 SG CYS A 118 101.528 59.901 142.412 1.00358.69 S ATOM 702 SG CYS A 121 103.459 62.884 141.674 1.00374.01 S ATOM 16340 SG CYS B1108 57.834 81.128 131.733 1.00189.89 S ATOM 16362 SG CYS B1111 60.744 78.962 132.342 1.00183.98 S ATOM 16432 SG CYS B1133 57.234 77.450 131.430 1.00232.83 S ATOM 16456 SG CYS B1136 57.883 78.600 134.838 1.00222.34 S ATOM 17385 SG CYS C 90 23.460 85.838 59.992 1.00203.16 S ATOM 17401 SG CYS C 93 22.471 82.138 60.552 1.00224.70 S ATOM 17434 SG CYS C 99 23.303 82.203 57.368 1.00189.51 S ATOM 24358 SG CYS I 76 117.609 105.715 67.377 1.00167.83 S ATOM 24379 SG CYS I 79 114.003 105.650 66.143 1.00178.64 S ATOM 24557 SG CYS I 103 115.415 102.652 67.999 1.00172.53 S ATOM 24592 SG CYS I 108 116.551 103.499 64.446 1.00174.16 S ATOM 23864 SG CYS I 7 138.374 40.330 85.742 1.00189.96 S ATOM 23890 SG CYS I 10 135.798 37.980 86.872 1.00204.85 S ATOM 24024 SG CYS I 29 137.267 40.566 89.403 1.00205.16 S ATOM 24049 SG CYS I 32 139.127 37.514 88.456 1.00197.09 S ATOM 24699 SG CYS J 7 55.209 79.789 47.136 1.00148.40 S ATOM 24723 SG CYS J 10 54.507 84.256 45.857 1.00166.92 S ATOM 24980 SG CYS J 44 57.677 83.208 45.826 1.00158.43 S ATOM 24986 SG CYS J 45 55.643 81.014 43.594 1.00164.97 S ATOM 25870 SG CYS L 12 46.077 41.217 68.142 1.00194.02 S ATOM 25888 SG CYS L 15 44.590 38.922 65.573 1.00173.03 S ATOM 25972 SG CYS L 29 43.432 38.881 69.208 1.00206.06 S ATOM 25988 SG CYS L 32 46.888 37.416 68.310 1.00208.68 S Time building chain proxies: 6.75, per 1000 atoms: 0.19 Number of scatterers: 35567 At special positions: 0 Unit cell: (187, 171.6, 188.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 218 16.00 P 67 15.00 Mg 1 11.99 O 6593 8.00 N 6235 7.00 C 22444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 56 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A 985 " pdb="ZN ZN A1503 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1044 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1031 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 118 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 100 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1133 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1108 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1136 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " Number of angles added : 40 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8622 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 53 sheets defined 37.2% alpha, 19.1% beta 26 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.567A pdb=" N LYS A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.527A pdb=" N THR A 125 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.437A pdb=" N TRP A 170 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.603A pdb=" N TYR A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.365A pdb=" N ILE A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 4.167A pdb=" N LEU A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.931A pdb=" N PHE A 444 " --> pdb=" O CYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.514A pdb=" N ASP A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.851A pdb=" N LEU A 477 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 504 removed outlier: 4.514A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.722A pdb=" N MET A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 removed outlier: 3.739A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 599 through 619 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.680A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 658 Processing helix chain 'A' and resid 659 through 660 No H-bonds generated for 'chain 'A' and resid 659 through 660' Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.583A pdb=" N SER A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.330A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 4.405A pdb=" N ASP A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 4.200A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 765 through 770 removed outlier: 3.623A pdb=" N ASN A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 825 through 840 removed outlier: 4.040A pdb=" N GLY A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 892 Processing helix chain 'A' and resid 903 through 913 Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.872A pdb=" N LEU A 933 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 935' Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 957 through 959 No H-bonds generated for 'chain 'A' and resid 957 through 959' Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.722A pdb=" N ARG A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1073 removed outlier: 4.369A pdb=" N ILE A1063 " --> pdb=" O GLU A1059 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Proline residue: A1069 - end of helix Processing helix chain 'A' and resid 1121 through 1130 Processing helix chain 'A' and resid 1131 through 1134 Processing helix chain 'A' and resid 1150 through 1175 removed outlier: 7.932A pdb=" N ILE A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N ASP A1157 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A1158 " --> pdb=" O TYR A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.861A pdb=" N LEU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 Processing helix chain 'A' and resid 1215 through 1223 Processing helix chain 'A' and resid 1224 through 1236 Processing helix chain 'A' and resid 1243 through 1250 Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.764A pdb=" N LEU B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 191 through 197 removed outlier: 3.823A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 322 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.579A pdb=" N LEU B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 405 through 431 removed outlier: 3.910A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.603A pdb=" N TYR B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.610A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.716A pdb=" N PHE B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 600 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 668 removed outlier: 3.915A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 668' Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.780A pdb=" N GLU B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.594A pdb=" N PHE B 695 " --> pdb=" O ASP B 692 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 696 " --> pdb=" O LEU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.962A pdb=" N VAL B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 763 through 767 removed outlier: 4.138A pdb=" N LEU B 766 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 767 " --> pdb=" O GLU B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 929 through 933 Processing helix chain 'B' and resid 949 through 955 removed outlier: 3.888A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 971 Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1088 through 1097 removed outlier: 3.959A pdb=" N LEU B1092 " --> pdb=" O ALA B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1162 removed outlier: 3.530A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.608A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.530A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.917A pdb=" N THR C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.541A pdb=" N ILE C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.541A pdb=" N ALA C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 238' Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.836A pdb=" N PHE D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 4.567A pdb=" N TYR D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 127 " --> pdb=" O TYR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.506A pdb=" N ARG D 143 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.689A pdb=" N CYS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 4.135A pdb=" N VAL D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 181 removed outlier: 3.607A pdb=" N LYS D 181 " --> pdb=" O PRO D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.738A pdb=" N LEU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 23 through 40 removed outlier: 4.061A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE G 30 " --> pdb=" O ARG G 26 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 removed outlier: 4.313A pdb=" N TYR G 134 " --> pdb=" O MET G 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.662A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.507A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG K 52 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.568A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 101 through 105 Processing helix chain 'M' and resid 246 through 252 removed outlier: 3.527A pdb=" N ILE M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 288 removed outlier: 4.431A pdb=" N LEU M 287 " --> pdb=" O ASN M 283 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY M 288 " --> pdb=" O ALA M 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 283 through 288' Processing helix chain 'M' and resid 292 through 305 Processing helix chain 'M' and resid 310 through 314 Processing helix chain 'M' and resid 315 through 324 removed outlier: 3.625A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 339 Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.511A pdb=" N PHE M 350 " --> pdb=" O ASP M 346 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 377 Processing helix chain 'M' and resid 408 through 412 removed outlier: 3.552A pdb=" N VAL M 412 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 433 Processing helix chain 'M' and resid 448 through 461 removed outlier: 3.530A pdb=" N ASN M 452 " --> pdb=" O THR M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 480 Processing helix chain 'M' and resid 494 through 503 removed outlier: 3.521A pdb=" N GLY M 503 " --> pdb=" O ARG M 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 520 Processing helix chain 'M' and resid 561 through 571 removed outlier: 4.305A pdb=" N LYS M 571 " --> pdb=" O GLN M 567 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 639 removed outlier: 3.535A pdb=" N ILE M 636 " --> pdb=" O ASN M 632 " (cutoff:3.500A) Processing helix chain 'M' and resid 645 through 662 removed outlier: 4.296A pdb=" N PHE M 649 " --> pdb=" O GLU M 645 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 678 removed outlier: 3.760A pdb=" N ALA M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU M 671 " --> pdb=" O ARG M 667 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN M 672 " --> pdb=" O ASP M 668 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER M 678 " --> pdb=" O LEU M 674 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.682A pdb=" N LEU M 691 " --> pdb=" O VAL M 687 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 720 removed outlier: 3.770A pdb=" N MET M 705 " --> pdb=" O TYR M 701 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 759 Processing helix chain 'M' and resid 788 through 792 removed outlier: 3.752A pdb=" N ILE M 792 " --> pdb=" O PRO M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 800 through 807 removed outlier: 3.529A pdb=" N LYS M 806 " --> pdb=" O HIS M 802 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY M 807 " --> pdb=" O PHE M 803 " (cutoff:3.500A) Processing helix chain 'M' and resid 821 through 826 Processing helix chain 'M' and resid 870 through 881 removed outlier: 4.256A pdb=" N MET M 880 " --> pdb=" O PHE M 876 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE M 881 " --> pdb=" O VAL M 877 " (cutoff:3.500A) Processing helix chain 'M' and resid 884 through 899 removed outlier: 3.617A pdb=" N ILE M 888 " --> pdb=" O THR M 884 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR M 890 " --> pdb=" O GLY M 886 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 921 removed outlier: 3.583A pdb=" N LEU M 909 " --> pdb=" O SER M 905 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 969 Processing helix chain 'M' and resid 999 through 1017 Processing helix chain 'M' and resid 1021 through 1027 removed outlier: 3.696A pdb=" N ILE M1025 " --> pdb=" O ASN M1021 " (cutoff:3.500A) Processing helix chain 'M' and resid 1041 through 1071 removed outlier: 3.724A pdb=" N CYS M1070 " --> pdb=" O PHE M1066 " (cutoff:3.500A) Processing helix chain 'M' and resid 1072 through 1089 Processing helix chain 'M' and resid 1090 through 1093 Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1239 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 4.167A pdb=" N GLY A 72 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 221 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N TYR A 78 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N GLY A 219 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 134 removed outlier: 3.658A pdb=" N VAL A 147 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 189 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.590A pdb=" N LYS A 316 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 318 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B1073 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 3.602A pdb=" N ASN A 410 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 454 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL A 434 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 325 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU A 436 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 327 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 340 removed outlier: 3.602A pdb=" N ASN A 410 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 454 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.800A pdb=" N ILE A 529 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.482A pdb=" N VAL A 565 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.577A pdb=" N GLY A 748 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.443A pdb=" N ASN A 852 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A 858 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 927 through 928 removed outlier: 7.106A pdb=" N GLU A1106 " --> pdb=" O TRP A1089 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP A1089 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR A1108 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE A1087 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS A1110 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A1085 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1112 " --> pdb=" O LYS A1083 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 954 through 955 removed outlier: 6.689A pdb=" N LEU A 954 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1022 through 1028 removed outlier: 4.297A pdb=" N ASP A1022 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A1024 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 962 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR I 44 " --> pdb=" O ILE A 965 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1261 through 1264 Processing sheet with id=AB7, first strand: chain 'B' and resid 94 through 102 removed outlier: 6.157A pdb=" N VAL B 95 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU B 139 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE B 97 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN B 137 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU B 99 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 135 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 173 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB9, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AC1, first strand: chain 'B' and resid 398 through 401 removed outlier: 5.925A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.860A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 249 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.586A pdb=" N GLU B 660 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC5, first strand: chain 'B' and resid 558 through 559 removed outlier: 7.344A pdb=" N VAL B 574 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU B 583 " --> pdb=" O HIS B 572 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS B 572 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS B 573 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 620 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 575 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.751A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 881 " --> pdb=" O MET B 854 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.751A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.130A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE B 946 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 775 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.592A pdb=" N ILE B 861 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1103 through 1108 Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.827A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU C 271 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR C 185 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 126 through 127 removed outlier: 5.285A pdb=" N CYS C 112 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN C 161 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU C 162 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS C 164 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 52 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AD5, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.677A pdb=" N ASP C 193 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C 260 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.725A pdb=" N GLN C 229 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 55 through 58 removed outlier: 3.689A pdb=" N THR E 55 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG E 96 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.811A pdb=" N GLU E 142 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.975A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN G 76 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU G 54 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.975A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU G 68 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 87 through 92 removed outlier: 3.604A pdb=" N TYR G 111 " --> pdb=" O ALA G 162 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 164 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER G 165 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 147 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 8 through 17 removed outlier: 6.933A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 15 through 18 removed outlier: 3.808A pdb=" N ALA I 28 " --> pdb=" O TYR I 15 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.873A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 39 through 43 Processing sheet with id=AE8, first strand: chain 'M' and resid 218 through 221 removed outlier: 4.198A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL M 195 " --> pdb=" O MET M 218 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA M 125 " --> pdb=" O PHE M 115 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE M 115 " --> pdb=" O ALA M 125 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU M 127 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL M 113 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG M 133 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP M 107 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU M 165 " --> pdb=" O LYS M 184 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG M 258 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 218 through 221 removed outlier: 4.198A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL M 195 " --> pdb=" O MET M 218 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE M 123 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 391 through 400 removed outlier: 6.673A pdb=" N ARG M 383 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N CYS M 381 " --> pdb=" O PRO M 396 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU M 398 " --> pdb=" O MET M 379 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N MET M 379 " --> pdb=" O LEU M 398 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE M 415 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN M 382 " --> pdb=" O PHE M 415 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 435 through 438 removed outlier: 3.569A pdb=" N SER M 437 " --> pdb=" O LYS M 444 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 526 through 530 removed outlier: 3.659A pdb=" N VAL M 620 " --> pdb=" O ARG M 526 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU M 618 " --> pdb=" O THR M 528 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN M 619 " --> pdb=" O ARG M 584 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG M 584 " --> pdb=" O ASN M 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE M 592 " --> pdb=" O PHE M 581 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 543 through 546 Processing sheet with id=AF5, first strand: chain 'M' and resid 627 through 631 removed outlier: 4.437A pdb=" N MET M 627 " --> pdb=" O ILE M 730 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY M 728 " --> pdb=" O CYS M 629 " (cutoff:3.500A) removed outlier: 11.416A pdb=" N LEU M 631 " --> pdb=" O PRO M 726 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 733 through 735 Processing sheet with id=AF7, first strand: chain 'M' and resid 745 through 746 removed outlier: 3.532A pdb=" N VAL M 746 " --> pdb=" O ASP M 796 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 748 through 751 removed outlier: 4.706A pdb=" N VAL M 748 " --> pdb=" O VAL M 775 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL M 750 " --> pdb=" O SER M 773 " (cutoff:3.500A) 1431 hydrogen bonds defined for protein. 4035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11374 1.34 - 1.46: 6726 1.46 - 1.58: 17811 1.58 - 1.70: 129 1.70 - 1.82: 331 Bond restraints: 36371 Sorted by residual: bond pdb=" C3' DT N 40 " pdb=" O3' DT N 40 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" C1' DT N 34 " pdb=" N1 DT N 34 " ideal model delta sigma weight residual 1.490 1.529 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" C1' DT Q 29 " pdb=" N1 DT Q 29 " ideal model delta sigma weight residual 1.490 1.524 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C LEU A 49 " pdb=" N PRO A 50 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" C3' DA N 25 " pdb=" O3' DA N 25 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 36366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 49126 1.50 - 3.00: 415 3.00 - 4.50: 53 4.50 - 6.00: 10 6.00 - 7.49: 2 Bond angle restraints: 49606 Sorted by residual: angle pdb=" C3' DG N 33 " pdb=" O3' DG N 33 " pdb=" P DT N 34 " ideal model delta sigma weight residual 120.20 124.00 -3.80 1.50e+00 4.44e-01 6.43e+00 angle pdb=" C LYS M 82 " pdb=" N THR M 83 " pdb=" CA THR M 83 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.93e+00 angle pdb=" C PRO A 761 " pdb=" N ARG A 762 " pdb=" CA ARG A 762 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.49e+00 angle pdb=" C GLN F 107 " pdb=" N ARG F 108 " pdb=" CA ARG F 108 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.04e+00 angle pdb=" C3' DT N 40 " pdb=" O3' DT N 40 " pdb=" P DC N 41 " ideal model delta sigma weight residual 120.20 123.53 -3.33 1.50e+00 4.44e-01 4.92e+00 ... (remaining 49601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 21427 35.01 - 70.02: 305 70.02 - 105.02: 9 105.02 - 140.03: 0 140.03 - 175.04: 4 Dihedral angle restraints: 21745 sinusoidal: 8450 harmonic: 13295 Sorted by residual: dihedral pdb=" C4' DT N 40 " pdb=" C3' DT N 40 " pdb=" O3' DT N 40 " pdb=" P DC N 41 " ideal model delta sinusoidal sigma weight residual -140.00 35.04 -175.04 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA N 25 " pdb=" C3' DA N 25 " pdb=" O3' DA N 25 " pdb=" P DG N 26 " ideal model delta sinusoidal sigma weight residual 220.00 53.39 166.61 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT Q 24 " pdb=" C3' DT Q 24 " pdb=" O3' DT Q 24 " pdb=" P DC Q 25 " ideal model delta sinusoidal sigma weight residual 220.00 75.39 144.61 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 21742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3702 0.026 - 0.053: 1284 0.053 - 0.079: 355 0.079 - 0.106: 295 0.106 - 0.132: 131 Chirality restraints: 5767 Sorted by residual: chirality pdb=" P DT N 34 " pdb=" OP1 DT N 34 " pdb=" OP2 DT N 34 " pdb=" O5' DT N 34 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE M 539 " pdb=" N ILE M 539 " pdb=" C ILE M 539 " pdb=" CB ILE M 539 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE G 123 " pdb=" N ILE G 123 " pdb=" C ILE G 123 " pdb=" CB ILE G 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 5764 not shown) Planarity restraints: 6108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG N 27 " -0.019 2.00e-02 2.50e+03 8.72e-03 2.28e+00 pdb=" N9 DG N 27 " 0.009 2.00e-02 2.50e+03 pdb=" C8 DG N 27 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DG N 27 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG N 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG N 27 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG N 27 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG N 27 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG N 27 " 0.013 2.00e-02 2.50e+03 pdb=" N2 DG N 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG N 27 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG N 27 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 28 " 0.018 2.00e-02 2.50e+03 8.70e-03 1.89e+00 pdb=" N1 DT N 28 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DT N 28 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT N 28 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT N 28 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT N 28 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT N 28 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT N 28 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT N 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT N 28 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 33 " 0.015 2.00e-02 2.50e+03 7.94e-03 1.89e+00 pdb=" N9 DG N 33 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DG N 33 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG N 33 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 33 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 33 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG N 33 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DG N 33 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG N 33 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG N 33 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG N 33 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG N 33 " -0.000 2.00e-02 2.50e+03 ... (remaining 6105 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 273 2.62 - 3.19: 29677 3.19 - 3.76: 52376 3.76 - 4.33: 69838 4.33 - 4.90: 118146 Nonbonded interactions: 270310 Sorted by model distance: nonbonded pdb=" O3' A O 10 " pdb="MG MG A1502 " model vdw 2.052 2.170 nonbonded pdb=" OD2 ASP H 10 " pdb=" OG SER H 34 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP B 845 " pdb=" OH TYR L 10 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU C 191 " pdb=" OG SER C 265 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 902 " pdb=" OD1 ASN A 907 " model vdw 2.263 3.040 ... (remaining 270305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 34.530 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.646 36406 Z= 0.189 Angle : 0.445 24.868 49646 Z= 0.204 Chirality : 0.038 0.132 5767 Planarity : 0.003 0.033 6108 Dihedral : 10.836 175.039 13123 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.44 % Allowed : 1.78 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 4502 helix: 1.88 (0.14), residues: 1465 sheet: 0.42 (0.21), residues: 687 loop : -1.00 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.009 0.001 TYR K 87 PHE 0.008 0.001 PHE J 8 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.000 HIS A 743 Details of bonding type rmsd covalent geometry : bond 0.00156 (36371) covalent geometry : angle 0.37704 (49606) hydrogen bonds : bond 0.20182 ( 1435) hydrogen bonds : angle 6.65204 ( 4163) metal coordination : bond 0.15939 ( 35) metal coordination : angle 8.34977 ( 40) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 356 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9260 (mt) cc_final: 0.8901 (pt) REVERT: A 150 ASN cc_start: 0.9664 (t0) cc_final: 0.9438 (t0) REVERT: A 311 ASP cc_start: 0.9145 (m-30) cc_final: 0.8739 (p0) REVERT: A 513 MET cc_start: 0.9172 (tpp) cc_final: 0.8844 (tpp) REVERT: A 706 ASP cc_start: 0.9024 (m-30) cc_final: 0.8804 (m-30) REVERT: A 922 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8811 (pm20) REVERT: A 925 MET cc_start: 0.8590 (mmt) cc_final: 0.8259 (mpp) REVERT: A 1134 MET cc_start: 0.8590 (mmm) cc_final: 0.8201 (mpp) REVERT: B 527 ASN cc_start: 0.8992 (p0) cc_final: 0.8667 (t0) REVERT: E 18 MET cc_start: 0.9355 (mmt) cc_final: 0.9114 (mmm) REVERT: E 127 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7859 (mp0) REVERT: E 130 MET cc_start: 0.9499 (mmm) cc_final: 0.9204 (mmp) REVERT: G 12 THR cc_start: 0.8372 (p) cc_final: 0.8028 (p) REVERT: G 163 LEU cc_start: 0.7306 (tt) cc_final: 0.7069 (mt) REVERT: H 41 MET cc_start: 0.9216 (ttp) cc_final: 0.8656 (tmm) REVERT: H 120 LEU cc_start: 0.9488 (mt) cc_final: 0.9265 (mm) REVERT: I 65 ASP cc_start: 0.8336 (t0) cc_final: 0.8053 (t0) REVERT: I 83 GLU cc_start: 0.8878 (tt0) cc_final: 0.8007 (tt0) REVERT: J 29 TYR cc_start: 0.8479 (m-80) cc_final: 0.8017 (m-80) REVERT: L 49 GLU cc_start: 0.8449 (tt0) cc_final: 0.8231 (tm-30) REVERT: M 416 MET cc_start: 0.8758 (ttp) cc_final: 0.8314 (tpp) REVERT: M 1063 MET cc_start: 0.8993 (mmp) cc_final: 0.8638 (tpp) outliers start: 15 outliers final: 4 residues processed: 370 average time/residue: 0.2139 time to fit residues: 125.3011 Evaluate side-chains 232 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain J residue 8 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.4980 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 20.0000 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN A 657 GLN ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A 857 GLN A1182 HIS A1219 GLN A1227 GLN B 220 GLN B 222 GLN B 355 HIS B 414 HIS B 477 ASN B 543 GLN B 577 ASN B 600 GLN B 652 HIS B 718 GLN B 724 GLN B 749 GLN B 771 ASN B 779 HIS B 804 GLN B1003 GLN B1042 HIS B1091 ASN C 229 GLN C 280 GLN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN G 65 GLN H 124 GLN I 12 ASN I 80 GLN K 89 GLN K 104 GLN L 28 GLN L 47 GLN M 84 HIS M 277 GLN M 298 GLN M 304 HIS M 478 GLN M 653 GLN M 710 HIS M 873 HIS M 913 ASN M1059 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.058669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.042002 restraints weight = 222149.601| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.87 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 36406 Z= 0.291 Angle : 0.686 11.391 49646 Z= 0.342 Chirality : 0.043 0.163 5767 Planarity : 0.004 0.043 6108 Dihedral : 12.951 176.604 5682 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.46 % Allowed : 5.00 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.13), residues: 4502 helix: 1.66 (0.14), residues: 1527 sheet: 0.23 (0.20), residues: 733 loop : -1.01 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 182 TYR 0.019 0.002 TYR A 605 PHE 0.020 0.002 PHE C 188 TRP 0.014 0.002 TRP B 514 HIS 0.008 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00634 (36371) covalent geometry : angle 0.66949 (49606) hydrogen bonds : bond 0.04658 ( 1435) hydrogen bonds : angle 4.95154 ( 4163) metal coordination : bond 0.01520 ( 35) metal coordination : angle 5.32241 ( 40) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.9111 (m-30) cc_final: 0.8739 (p0) REVERT: A 409 MET cc_start: 0.8614 (mmm) cc_final: 0.8346 (mmm) REVERT: A 513 MET cc_start: 0.9287 (tpp) cc_final: 0.8847 (tpp) REVERT: A 706 ASP cc_start: 0.8966 (m-30) cc_final: 0.8731 (m-30) REVERT: A 745 MET cc_start: 0.8788 (mtm) cc_final: 0.8586 (mtm) REVERT: A 922 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8852 (pm20) REVERT: A 1134 MET cc_start: 0.8788 (mmm) cc_final: 0.8212 (mpp) REVERT: B 786 ASP cc_start: 0.8941 (m-30) cc_final: 0.8420 (t0) REVERT: D 130 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8112 (p) REVERT: E 18 MET cc_start: 0.9237 (mmt) cc_final: 0.8942 (mmm) REVERT: E 48 MET cc_start: 0.8794 (mmm) cc_final: 0.8573 (mmp) REVERT: E 103 GLN cc_start: 0.8815 (mt0) cc_final: 0.8610 (pt0) REVERT: E 127 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8121 (mp0) REVERT: E 130 MET cc_start: 0.9427 (mmm) cc_final: 0.9195 (mmp) REVERT: G 39 GLU cc_start: 0.9047 (pt0) cc_final: 0.8841 (pp20) REVERT: G 56 ASN cc_start: 0.8777 (t0) cc_final: 0.8544 (t0) REVERT: G 65 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8139 (mm-40) REVERT: G 163 LEU cc_start: 0.7359 (tt) cc_final: 0.7103 (mt) REVERT: H 121 MET cc_start: 0.9161 (ttp) cc_final: 0.7904 (tmm) REVERT: I 65 ASP cc_start: 0.8381 (t0) cc_final: 0.8176 (t0) REVERT: I 97 MET cc_start: 0.9034 (mmm) cc_final: 0.8541 (mmm) REVERT: J 29 TYR cc_start: 0.8693 (m-80) cc_final: 0.8214 (m-80) REVERT: K 48 MET cc_start: 0.8851 (mmm) cc_final: 0.8284 (mmm) REVERT: M 325 MET cc_start: 0.7908 (ptt) cc_final: 0.6732 (pmm) REVERT: M 416 MET cc_start: 0.8753 (ttp) cc_final: 0.8229 (tpp) REVERT: M 486 MET cc_start: 0.8580 (mpp) cc_final: 0.8274 (mmp) REVERT: M 648 MET cc_start: 0.9355 (tmm) cc_final: 0.9127 (tmm) REVERT: M 929 GLU cc_start: 0.8106 (tp30) cc_final: 0.7755 (tp30) outliers start: 50 outliers final: 27 residues processed: 262 average time/residue: 0.1905 time to fit residues: 83.7414 Evaluate side-chains 227 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 637 CYS Chi-restraints excluded: chain M residue 748 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 348 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN A 485 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 316 HIS B 381 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.058209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.041532 restraints weight = 220925.035| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.87 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36406 Z= 0.196 Angle : 0.559 13.445 49646 Z= 0.280 Chirality : 0.041 0.165 5767 Planarity : 0.003 0.041 6108 Dihedral : 12.933 174.640 5680 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.35 % Allowed : 6.29 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.13), residues: 4502 helix: 1.93 (0.14), residues: 1523 sheet: 0.09 (0.19), residues: 742 loop : -1.05 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1141 TYR 0.016 0.001 TYR K 87 PHE 0.014 0.001 PHE J 8 TRP 0.017 0.001 TRP A1139 HIS 0.006 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00432 (36371) covalent geometry : angle 0.54032 (49606) hydrogen bonds : bond 0.03864 ( 1435) hydrogen bonds : angle 4.58493 ( 4163) metal coordination : bond 0.01244 ( 35) metal coordination : angle 5.05288 ( 40) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.9243 (tpp) cc_final: 0.8834 (tpp) REVERT: A 706 ASP cc_start: 0.8954 (m-30) cc_final: 0.8692 (m-30) REVERT: A 745 MET cc_start: 0.8778 (mtm) cc_final: 0.8566 (mtm) REVERT: A 922 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8802 (pm20) REVERT: A 1134 MET cc_start: 0.8812 (mmm) cc_final: 0.8219 (mpp) REVERT: B 557 MET cc_start: 0.8560 (ttp) cc_final: 0.8305 (ttp) REVERT: B 786 ASP cc_start: 0.8995 (m-30) cc_final: 0.8423 (t0) REVERT: B 799 MET cc_start: 0.9214 (ttm) cc_final: 0.8930 (ttt) REVERT: E 18 MET cc_start: 0.9223 (mmt) cc_final: 0.8919 (mmm) REVERT: E 48 MET cc_start: 0.8783 (mmm) cc_final: 0.8512 (mmm) REVERT: E 76 LYS cc_start: 0.9090 (tppt) cc_final: 0.8866 (tppt) REVERT: E 127 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8063 (mp0) REVERT: E 130 MET cc_start: 0.9472 (mmm) cc_final: 0.9191 (mmp) REVERT: F 69 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8750 (mt-10) REVERT: G 65 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8299 (mm-40) REVERT: G 163 LEU cc_start: 0.7347 (tt) cc_final: 0.7083 (mt) REVERT: H 121 MET cc_start: 0.9132 (ttp) cc_final: 0.7782 (tmm) REVERT: I 97 MET cc_start: 0.9041 (mmm) cc_final: 0.8500 (mmm) REVERT: J 29 TYR cc_start: 0.8773 (m-80) cc_final: 0.8303 (m-80) REVERT: M 325 MET cc_start: 0.8085 (ptt) cc_final: 0.7666 (ptt) REVERT: M 416 MET cc_start: 0.8851 (ttp) cc_final: 0.8291 (tpp) REVERT: M 486 MET cc_start: 0.8528 (mpp) cc_final: 0.8244 (mpp) REVERT: M 608 MET cc_start: 0.8031 (tpp) cc_final: 0.7784 (tpp) REVERT: M 849 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4811 (mmm) REVERT: M 929 GLU cc_start: 0.8368 (tp30) cc_final: 0.7878 (tp30) REVERT: M 1063 MET cc_start: 0.9184 (mmm) cc_final: 0.8957 (mmm) outliers start: 46 outliers final: 30 residues processed: 242 average time/residue: 0.1780 time to fit residues: 74.3169 Evaluate side-chains 226 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 849 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 407 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 365 optimal weight: 6.9990 chunk 431 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN B 771 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN L 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.056829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040040 restraints weight = 221274.332| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.80 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36406 Z= 0.248 Angle : 0.616 10.819 49646 Z= 0.308 Chirality : 0.041 0.171 5767 Planarity : 0.004 0.038 6108 Dihedral : 13.021 175.036 5680 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.02 % Allowed : 6.64 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.13), residues: 4502 helix: 1.89 (0.14), residues: 1525 sheet: -0.07 (0.19), residues: 729 loop : -1.10 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 269 TYR 0.017 0.001 TYR K 87 PHE 0.019 0.001 PHE C 268 TRP 0.010 0.001 TRP A1139 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00540 (36371) covalent geometry : angle 0.59821 (49606) hydrogen bonds : bond 0.04181 ( 1435) hydrogen bonds : angle 4.53831 ( 4163) metal coordination : bond 0.01303 ( 35) metal coordination : angle 5.24119 ( 40) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8067 (mpp) cc_final: 0.7626 (mpp) REVERT: A 309 MET cc_start: 0.9562 (mmm) cc_final: 0.9315 (tpp) REVERT: A 402 MET cc_start: 0.7717 (ptt) cc_final: 0.6957 (ppp) REVERT: A 513 MET cc_start: 0.9273 (tpp) cc_final: 0.8862 (tpp) REVERT: A 706 ASP cc_start: 0.8965 (m-30) cc_final: 0.8697 (m-30) REVERT: A 745 MET cc_start: 0.8865 (mtm) cc_final: 0.8456 (mtm) REVERT: A 925 MET cc_start: 0.8771 (mmp) cc_final: 0.8440 (mmp) REVERT: A 1134 MET cc_start: 0.8696 (mmm) cc_final: 0.8194 (mpp) REVERT: B 295 MET cc_start: 0.9111 (mmt) cc_final: 0.8885 (mmt) REVERT: B 534 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8733 (ttt) REVERT: B 786 ASP cc_start: 0.9009 (m-30) cc_final: 0.8457 (t0) REVERT: C 33 MET cc_start: 0.8857 (tpp) cc_final: 0.8641 (tpp) REVERT: C 200 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8476 (ttp) REVERT: C 201 MET cc_start: 0.9001 (ppp) cc_final: 0.8727 (ppp) REVERT: E 18 MET cc_start: 0.9248 (mmt) cc_final: 0.8936 (mmm) REVERT: E 48 MET cc_start: 0.8668 (mmm) cc_final: 0.8461 (mmp) REVERT: E 127 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8109 (mp0) REVERT: E 130 MET cc_start: 0.9473 (mmm) cc_final: 0.9162 (mmp) REVERT: E 135 LYS cc_start: 0.9266 (tppt) cc_final: 0.9060 (tppt) REVERT: F 69 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8901 (mp0) REVERT: G 103 LYS cc_start: 0.4516 (mppt) cc_final: 0.4164 (mmmt) REVERT: G 163 LEU cc_start: 0.7291 (tt) cc_final: 0.6987 (mt) REVERT: H 121 MET cc_start: 0.9168 (ttp) cc_final: 0.7641 (tmm) REVERT: I 4 MET cc_start: 0.8359 (ppp) cc_final: 0.8067 (ppp) REVERT: I 75 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7546 (tpp80) REVERT: I 83 GLU cc_start: 0.8919 (tp30) cc_final: 0.8645 (tp30) REVERT: I 97 MET cc_start: 0.9082 (mmm) cc_final: 0.8608 (mmm) REVERT: J 29 TYR cc_start: 0.8878 (m-80) cc_final: 0.8461 (m-80) REVERT: M 325 MET cc_start: 0.7869 (ptt) cc_final: 0.7318 (ptt) REVERT: M 416 MET cc_start: 0.8795 (ttp) cc_final: 0.8445 (tpp) REVERT: M 486 MET cc_start: 0.8556 (mpp) cc_final: 0.8243 (mpp) REVERT: M 648 MET cc_start: 0.9327 (tmm) cc_final: 0.9057 (ppp) REVERT: M 929 GLU cc_start: 0.8535 (tp30) cc_final: 0.7909 (tp30) REVERT: M 1063 MET cc_start: 0.9356 (mmm) cc_final: 0.9106 (mmm) outliers start: 69 outliers final: 48 residues processed: 250 average time/residue: 0.1833 time to fit residues: 78.5955 Evaluate side-chains 235 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 585 TYR Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 278 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 287 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 344 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 423 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 412 optimal weight: 40.0000 chunk 443 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.056720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.039960 restraints weight = 222989.813| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.90 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36406 Z= 0.203 Angle : 0.565 14.325 49646 Z= 0.282 Chirality : 0.041 0.166 5767 Planarity : 0.003 0.041 6108 Dihedral : 12.974 174.134 5678 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.70 % Allowed : 7.34 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.13), residues: 4502 helix: 1.94 (0.14), residues: 1531 sheet: -0.12 (0.19), residues: 749 loop : -1.12 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 70 TYR 0.017 0.001 TYR K 87 PHE 0.014 0.001 PHE C 268 TRP 0.014 0.001 TRP B 229 HIS 0.006 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00450 (36371) covalent geometry : angle 0.54490 (49606) hydrogen bonds : bond 0.03657 ( 1435) hydrogen bonds : angle 4.42695 ( 4163) metal coordination : bond 0.01100 ( 35) metal coordination : angle 5.23376 ( 40) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8040 (mpp) cc_final: 0.7639 (mpp) REVERT: A 513 MET cc_start: 0.9261 (tpp) cc_final: 0.8890 (tpp) REVERT: A 706 ASP cc_start: 0.8943 (m-30) cc_final: 0.8670 (m-30) REVERT: A 745 MET cc_start: 0.8836 (mtm) cc_final: 0.8457 (mtm) REVERT: A 925 MET cc_start: 0.8841 (mmp) cc_final: 0.8518 (mmp) REVERT: B 223 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (mmm) REVERT: B 534 MET cc_start: 0.9088 (ttm) cc_final: 0.8731 (ttt) REVERT: B 786 ASP cc_start: 0.8970 (m-30) cc_final: 0.8430 (t0) REVERT: B 1025 MET cc_start: 0.8660 (tmm) cc_final: 0.8135 (tmm) REVERT: C 200 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8487 (ttt) REVERT: C 201 MET cc_start: 0.9046 (ppp) cc_final: 0.8700 (ppp) REVERT: E 18 MET cc_start: 0.9219 (mmt) cc_final: 0.8905 (mmm) REVERT: E 35 MET cc_start: 0.8761 (tpp) cc_final: 0.8536 (tpp) REVERT: E 48 MET cc_start: 0.8657 (mmm) cc_final: 0.8418 (mmp) REVERT: E 127 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8055 (mp0) REVERT: E 130 MET cc_start: 0.9469 (mmm) cc_final: 0.9143 (mmp) REVERT: F 69 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8913 (mp0) REVERT: G 163 LEU cc_start: 0.6884 (tt) cc_final: 0.6598 (mt) REVERT: H 39 MET cc_start: 0.7965 (mmm) cc_final: 0.7495 (mmm) REVERT: H 121 MET cc_start: 0.9130 (ttp) cc_final: 0.7560 (tmm) REVERT: I 4 MET cc_start: 0.8507 (ppp) cc_final: 0.8136 (ppp) REVERT: I 97 MET cc_start: 0.9040 (mmm) cc_final: 0.8729 (mmm) REVERT: J 29 TYR cc_start: 0.8877 (m-80) cc_final: 0.8474 (m-80) REVERT: M 325 MET cc_start: 0.7880 (ptt) cc_final: 0.7299 (ptt) REVERT: M 416 MET cc_start: 0.8816 (ttp) cc_final: 0.8496 (tpp) REVERT: M 486 MET cc_start: 0.8622 (mpp) cc_final: 0.8287 (mpp) REVERT: M 648 MET cc_start: 0.9306 (tmm) cc_final: 0.9027 (ppp) REVERT: M 849 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5161 (mmm) REVERT: M 1063 MET cc_start: 0.9354 (mmm) cc_final: 0.9069 (mmm) outliers start: 58 outliers final: 44 residues processed: 235 average time/residue: 0.1826 time to fit residues: 74.2327 Evaluate side-chains 234 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 839 MET Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 849 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 35 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 422 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 chunk 419 optimal weight: 50.0000 chunk 215 optimal weight: 10.0000 chunk 374 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN B 330 ASN B 771 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** M 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.056147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039306 restraints weight = 223569.850| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.80 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 36406 Z= 0.250 Angle : 0.609 11.288 49646 Z= 0.302 Chirality : 0.041 0.167 5767 Planarity : 0.004 0.046 6108 Dihedral : 13.010 174.342 5678 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.02 % Allowed : 7.78 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.13), residues: 4502 helix: 1.87 (0.14), residues: 1526 sheet: -0.17 (0.19), residues: 748 loop : -1.15 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 506 TYR 0.017 0.001 TYR K 87 PHE 0.016 0.001 PHE C 268 TRP 0.009 0.001 TRP B 229 HIS 0.007 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00550 (36371) covalent geometry : angle 0.59089 (49606) hydrogen bonds : bond 0.03988 ( 1435) hydrogen bonds : angle 4.48607 ( 4163) metal coordination : bond 0.01332 ( 35) metal coordination : angle 5.20814 ( 40) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8235 (mpp) cc_final: 0.7899 (mpp) REVERT: A 402 MET cc_start: 0.7805 (ptt) cc_final: 0.7085 (ppp) REVERT: A 513 MET cc_start: 0.9260 (tpp) cc_final: 0.8877 (tpp) REVERT: A 706 ASP cc_start: 0.8885 (m-30) cc_final: 0.8640 (m-30) REVERT: A 745 MET cc_start: 0.8865 (mtm) cc_final: 0.8453 (mtm) REVERT: A 925 MET cc_start: 0.8804 (mmp) cc_final: 0.8597 (mmp) REVERT: B 295 MET cc_start: 0.9143 (mmt) cc_final: 0.8899 (mmm) REVERT: B 534 MET cc_start: 0.9089 (ttm) cc_final: 0.8723 (ttt) REVERT: B 1025 MET cc_start: 0.8690 (tmm) cc_final: 0.8165 (tmm) REVERT: C 200 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8686 (ttt) REVERT: C 201 MET cc_start: 0.9091 (ppp) cc_final: 0.8533 (ppp) REVERT: E 18 MET cc_start: 0.9224 (mmt) cc_final: 0.8912 (mmm) REVERT: E 48 MET cc_start: 0.8525 (mmm) cc_final: 0.8308 (mmm) REVERT: E 89 MET cc_start: 0.9149 (ttt) cc_final: 0.8788 (tpt) REVERT: E 127 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7988 (mp0) REVERT: E 130 MET cc_start: 0.9470 (mmm) cc_final: 0.9132 (mmp) REVERT: F 69 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8926 (mp0) REVERT: G 103 LYS cc_start: 0.3877 (mppt) cc_final: 0.3626 (mmmt) REVERT: G 163 LEU cc_start: 0.6802 (tt) cc_final: 0.6547 (mt) REVERT: H 121 MET cc_start: 0.9163 (ttp) cc_final: 0.7566 (tmm) REVERT: I 4 MET cc_start: 0.8649 (ppp) cc_final: 0.8210 (ppp) REVERT: I 75 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7668 (tpp80) REVERT: I 97 MET cc_start: 0.9044 (mmm) cc_final: 0.8842 (mmm) REVERT: L 15 CYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8359 (p) REVERT: M 245 SER cc_start: 0.8827 (m) cc_final: 0.8462 (p) REVERT: M 325 MET cc_start: 0.8511 (ptt) cc_final: 0.7862 (ptt) REVERT: M 416 MET cc_start: 0.8790 (ttp) cc_final: 0.8359 (tpp) REVERT: M 486 MET cc_start: 0.8654 (mpp) cc_final: 0.8298 (mpp) REVERT: M 648 MET cc_start: 0.9391 (tmm) cc_final: 0.9103 (ppp) REVERT: M 735 MET cc_start: 0.6932 (tpp) cc_final: 0.6710 (tpt) REVERT: M 849 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.4886 (mmm) REVERT: M 1063 MET cc_start: 0.9452 (mmm) cc_final: 0.9157 (mmm) outliers start: 69 outliers final: 52 residues processed: 247 average time/residue: 0.1878 time to fit residues: 80.2895 Evaluate side-chains 238 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 839 MET Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 29 CYS Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 849 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 36 optimal weight: 3.9990 chunk 440 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 436 optimal weight: 8.9990 chunk 435 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 400 optimal weight: 20.0000 chunk 250 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 279 optimal weight: 0.0770 chunk 313 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.056948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.040222 restraints weight = 221439.169| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.83 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36406 Z= 0.114 Angle : 0.529 10.517 49646 Z= 0.264 Chirality : 0.040 0.161 5767 Planarity : 0.003 0.042 6108 Dihedral : 12.944 172.596 5678 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.43 % Allowed : 8.43 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.13), residues: 4502 helix: 2.03 (0.14), residues: 1534 sheet: -0.06 (0.19), residues: 749 loop : -1.10 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 506 TYR 0.019 0.001 TYR K 87 PHE 0.015 0.001 PHE J 8 TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00251 (36371) covalent geometry : angle 0.51480 (49606) hydrogen bonds : bond 0.03202 ( 1435) hydrogen bonds : angle 4.20844 ( 4163) metal coordination : bond 0.00702 ( 35) metal coordination : angle 4.38283 ( 40) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8120 (mpp) cc_final: 0.7808 (mpp) REVERT: A 402 MET cc_start: 0.7952 (ptt) cc_final: 0.7215 (ppp) REVERT: A 409 MET cc_start: 0.8426 (mmm) cc_final: 0.8195 (mmp) REVERT: A 513 MET cc_start: 0.9217 (tpp) cc_final: 0.8937 (tpp) REVERT: A 706 ASP cc_start: 0.8910 (m-30) cc_final: 0.8672 (m-30) REVERT: A 745 MET cc_start: 0.8876 (mtm) cc_final: 0.8531 (mtm) REVERT: A 925 MET cc_start: 0.8766 (mmp) cc_final: 0.8539 (mmp) REVERT: B 295 MET cc_start: 0.9154 (mmt) cc_final: 0.8923 (mmm) REVERT: B 534 MET cc_start: 0.9090 (ttm) cc_final: 0.8736 (ttt) REVERT: B 1025 MET cc_start: 0.8674 (tmm) cc_final: 0.8229 (tmm) REVERT: C 200 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8750 (ttp) REVERT: C 201 MET cc_start: 0.9069 (ppp) cc_final: 0.8346 (ppp) REVERT: E 18 MET cc_start: 0.9217 (mmt) cc_final: 0.8900 (mmm) REVERT: E 127 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7921 (mp0) REVERT: E 130 MET cc_start: 0.9475 (mmm) cc_final: 0.9115 (mmp) REVERT: F 69 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8898 (mp0) REVERT: G 64 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8073 (pm20) REVERT: G 163 LEU cc_start: 0.6931 (tt) cc_final: 0.6660 (mt) REVERT: H 39 MET cc_start: 0.7766 (mmm) cc_final: 0.7406 (mmm) REVERT: H 121 MET cc_start: 0.9097 (ttp) cc_final: 0.7447 (tmm) REVERT: I 4 MET cc_start: 0.8638 (ppp) cc_final: 0.8234 (ppp) REVERT: I 97 MET cc_start: 0.8989 (mmm) cc_final: 0.8775 (mmm) REVERT: J 29 TYR cc_start: 0.8840 (m-80) cc_final: 0.8533 (m-80) REVERT: M 325 MET cc_start: 0.8310 (ptt) cc_final: 0.7637 (ptt) REVERT: M 379 MET cc_start: 0.9448 (ppp) cc_final: 0.9130 (ppp) REVERT: M 416 MET cc_start: 0.8818 (ttp) cc_final: 0.8464 (tpp) REVERT: M 486 MET cc_start: 0.8703 (mpp) cc_final: 0.8354 (mpp) REVERT: M 617 MET cc_start: 0.8861 (tpt) cc_final: 0.7911 (tpp) REVERT: M 648 MET cc_start: 0.9324 (tmm) cc_final: 0.9052 (ppp) REVERT: M 735 MET cc_start: 0.7144 (tpp) cc_final: 0.6939 (tpp) REVERT: M 929 GLU cc_start: 0.8662 (tp30) cc_final: 0.7835 (tp30) REVERT: M 1063 MET cc_start: 0.9395 (mmm) cc_final: 0.9057 (mmm) outliers start: 49 outliers final: 35 residues processed: 232 average time/residue: 0.1994 time to fit residues: 79.2866 Evaluate side-chains 223 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 839 MET Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 29 CYS Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 39 optimal weight: 2.9990 chunk 385 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 306 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 437 optimal weight: 0.0060 chunk 253 optimal weight: 0.0030 chunk 109 optimal weight: 4.9990 chunk 288 optimal weight: 0.4980 chunk 260 optimal weight: 40.0000 chunk 217 optimal weight: 9.9990 overall best weight: 0.9008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.057417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.040756 restraints weight = 218646.538| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.89 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36406 Z= 0.092 Angle : 0.516 10.332 49646 Z= 0.256 Chirality : 0.040 0.246 5767 Planarity : 0.003 0.044 6108 Dihedral : 12.854 171.556 5678 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.99 % Allowed : 9.01 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.13), residues: 4502 helix: 2.08 (0.14), residues: 1532 sheet: 0.03 (0.19), residues: 736 loop : -1.02 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 28 TYR 0.018 0.001 TYR K 87 PHE 0.013 0.001 PHE J 8 TRP 0.009 0.001 TRP B 119 HIS 0.004 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00202 (36371) covalent geometry : angle 0.50542 (49606) hydrogen bonds : bond 0.02767 ( 1435) hydrogen bonds : angle 4.03253 ( 4163) metal coordination : bond 0.00449 ( 35) metal coordination : angle 3.75941 ( 40) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8083 (mpp) cc_final: 0.7786 (mpp) REVERT: A 402 MET cc_start: 0.8006 (ptt) cc_final: 0.7270 (ppp) REVERT: A 513 MET cc_start: 0.9171 (tpp) cc_final: 0.8903 (tpp) REVERT: A 706 ASP cc_start: 0.8905 (m-30) cc_final: 0.8663 (m-30) REVERT: A 745 MET cc_start: 0.8836 (mtm) cc_final: 0.8489 (mtm) REVERT: A 925 MET cc_start: 0.8719 (mmp) cc_final: 0.8356 (mmt) REVERT: A 1134 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7793 (mpp) REVERT: B 534 MET cc_start: 0.9098 (ttm) cc_final: 0.8774 (ttt) REVERT: B 557 MET cc_start: 0.8297 (ttt) cc_final: 0.7540 (tmm) REVERT: C 201 MET cc_start: 0.9056 (ppp) cc_final: 0.8272 (ppp) REVERT: E 18 MET cc_start: 0.9199 (mmt) cc_final: 0.8883 (mmm) REVERT: E 89 MET cc_start: 0.9137 (ttt) cc_final: 0.8930 (tpp) REVERT: E 130 MET cc_start: 0.9478 (mmm) cc_final: 0.9118 (mmp) REVERT: F 69 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8877 (mp0) REVERT: G 64 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8027 (pm20) REVERT: H 39 MET cc_start: 0.7817 (mmm) cc_final: 0.7453 (mmm) REVERT: H 121 MET cc_start: 0.9072 (ttp) cc_final: 0.7345 (tmm) REVERT: I 4 MET cc_start: 0.8583 (ppp) cc_final: 0.8171 (ppp) REVERT: I 97 MET cc_start: 0.9002 (mmm) cc_final: 0.8718 (mmm) REVERT: J 29 TYR cc_start: 0.8740 (m-80) cc_final: 0.8465 (m-80) REVERT: K 41 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9051 (m) REVERT: L 15 CYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8423 (p) REVERT: M 21 ILE cc_start: 0.9434 (pt) cc_final: 0.9070 (mm) REVERT: M 325 MET cc_start: 0.7924 (ptt) cc_final: 0.7210 (ptt) REVERT: M 416 MET cc_start: 0.8861 (ttp) cc_final: 0.8510 (tpp) REVERT: M 486 MET cc_start: 0.8692 (mpp) cc_final: 0.8341 (mpp) REVERT: M 608 MET cc_start: 0.8222 (tpp) cc_final: 0.7981 (tpp) REVERT: M 617 MET cc_start: 0.8989 (tpt) cc_final: 0.7999 (tpp) REVERT: M 880 MET cc_start: 0.9145 (mtm) cc_final: 0.8933 (mpp) REVERT: M 929 GLU cc_start: 0.8652 (tp30) cc_final: 0.7872 (tp30) REVERT: M 1063 MET cc_start: 0.9385 (mmm) cc_final: 0.9174 (tpp) outliers start: 34 outliers final: 26 residues processed: 217 average time/residue: 0.1996 time to fit residues: 73.7521 Evaluate side-chains 215 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 839 MET Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 849 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.1980 chunk 119 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 301 optimal weight: 50.0000 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.056214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039458 restraints weight = 222600.216| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.82 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36406 Z= 0.210 Angle : 0.604 15.884 49646 Z= 0.295 Chirality : 0.041 0.252 5767 Planarity : 0.003 0.043 6108 Dihedral : 12.903 173.872 5678 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.17 % Allowed : 9.30 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.13), residues: 4502 helix: 2.06 (0.14), residues: 1532 sheet: -0.10 (0.19), residues: 745 loop : -1.04 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 43 TYR 0.020 0.001 TYR K 87 PHE 0.013 0.001 PHE C 268 TRP 0.014 0.001 TRP B 229 HIS 0.014 0.001 HIS M 710 Details of bonding type rmsd covalent geometry : bond 0.00463 (36371) covalent geometry : angle 0.59042 (49606) hydrogen bonds : bond 0.03692 ( 1435) hydrogen bonds : angle 4.21923 ( 4163) metal coordination : bond 0.01073 ( 35) metal coordination : angle 4.45324 ( 40) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8185 (mpp) cc_final: 0.7898 (mpp) REVERT: A 513 MET cc_start: 0.9263 (tpp) cc_final: 0.8868 (tpp) REVERT: A 706 ASP cc_start: 0.8915 (m-30) cc_final: 0.8657 (m-30) REVERT: A 745 MET cc_start: 0.8902 (mtm) cc_final: 0.8438 (mtm) REVERT: A 925 MET cc_start: 0.8758 (mmp) cc_final: 0.8477 (mmm) REVERT: A 1134 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7388 (mmm) REVERT: B 295 MET cc_start: 0.9179 (mmt) cc_final: 0.8880 (mmm) REVERT: B 534 MET cc_start: 0.9104 (ttm) cc_final: 0.8746 (ttt) REVERT: C 201 MET cc_start: 0.9132 (ppp) cc_final: 0.8469 (ppp) REVERT: E 18 MET cc_start: 0.9229 (mmt) cc_final: 0.8912 (mmm) REVERT: E 130 MET cc_start: 0.9467 (mmm) cc_final: 0.9089 (mmp) REVERT: F 69 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8919 (mp0) REVERT: G 149 LEU cc_start: 0.6176 (mt) cc_final: 0.5508 (pp) REVERT: G 163 LEU cc_start: 0.7080 (tt) cc_final: 0.6517 (mm) REVERT: H 39 MET cc_start: 0.7910 (mmm) cc_final: 0.7506 (mmm) REVERT: H 121 MET cc_start: 0.9153 (ttp) cc_final: 0.7497 (tmm) REVERT: I 4 MET cc_start: 0.8675 (ppp) cc_final: 0.8226 (ppp) REVERT: I 75 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7576 (tpp80) REVERT: K 48 MET cc_start: 0.8917 (mmm) cc_final: 0.8639 (mmm) REVERT: L 15 CYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (p) REVERT: M 245 SER cc_start: 0.8878 (m) cc_final: 0.8487 (p) REVERT: M 325 MET cc_start: 0.8465 (ptt) cc_final: 0.7821 (ptt) REVERT: M 379 MET cc_start: 0.9413 (ppp) cc_final: 0.8959 (ppp) REVERT: M 416 MET cc_start: 0.8856 (ttp) cc_final: 0.8485 (tpp) REVERT: M 486 MET cc_start: 0.8687 (mpp) cc_final: 0.8306 (mpp) REVERT: M 608 MET cc_start: 0.8179 (tpp) cc_final: 0.7926 (tpp) REVERT: M 648 MET cc_start: 0.9366 (tmm) cc_final: 0.8982 (ppp) REVERT: M 735 MET cc_start: 0.6949 (tpp) cc_final: 0.6476 (tpt) REVERT: M 880 MET cc_start: 0.9129 (mtm) cc_final: 0.8861 (mpp) REVERT: M 929 GLU cc_start: 0.8601 (tp30) cc_final: 0.7853 (tp30) REVERT: M 1063 MET cc_start: 0.9441 (mmm) cc_final: 0.9116 (mmm) outliers start: 40 outliers final: 30 residues processed: 211 average time/residue: 0.1884 time to fit residues: 69.1483 Evaluate side-chains 214 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 29 CYS Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 849 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 278 optimal weight: 0.8980 chunk 338 optimal weight: 1.9990 chunk 176 optimal weight: 0.0670 chunk 132 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 301 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 23 optimal weight: 50.0000 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.057199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.040571 restraints weight = 221061.619| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.85 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 36406 Z= 0.095 Angle : 0.544 13.257 49646 Z= 0.265 Chirality : 0.040 0.258 5767 Planarity : 0.003 0.045 6108 Dihedral : 12.843 171.914 5678 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.85 % Allowed : 9.74 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.13), residues: 4502 helix: 2.12 (0.14), residues: 1532 sheet: 0.08 (0.20), residues: 739 loop : -1.00 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 28 TYR 0.017 0.001 TYR K 87 PHE 0.011 0.001 PHE G 101 TRP 0.016 0.001 TRP B 229 HIS 0.009 0.001 HIS M 710 Details of bonding type rmsd covalent geometry : bond 0.00213 (36371) covalent geometry : angle 0.53443 (49606) hydrogen bonds : bond 0.02801 ( 1435) hydrogen bonds : angle 4.01765 ( 4163) metal coordination : bond 0.00475 ( 35) metal coordination : angle 3.64719 ( 40) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9004 Ramachandran restraints generated. 4502 Oldfield, 0 Emsley, 4502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8021 (mpp) cc_final: 0.7726 (mpp) REVERT: A 402 MET cc_start: 0.8095 (ptt) cc_final: 0.7316 (ppp) REVERT: A 409 MET cc_start: 0.8410 (mmm) cc_final: 0.8103 (mmp) REVERT: A 513 MET cc_start: 0.9179 (tpp) cc_final: 0.8868 (tpp) REVERT: A 706 ASP cc_start: 0.8918 (m-30) cc_final: 0.8684 (m-30) REVERT: A 745 MET cc_start: 0.8827 (mtm) cc_final: 0.8486 (mtm) REVERT: A 925 MET cc_start: 0.8673 (mmp) cc_final: 0.8388 (mmt) REVERT: A 1134 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7780 (mpp) REVERT: B 534 MET cc_start: 0.9080 (ttm) cc_final: 0.8769 (ttt) REVERT: C 84 MET cc_start: 0.8559 (mtp) cc_final: 0.8292 (mtp) REVERT: C 201 MET cc_start: 0.9119 (ppp) cc_final: 0.8371 (ppp) REVERT: E 18 MET cc_start: 0.9194 (mmt) cc_final: 0.8878 (mmm) REVERT: E 130 MET cc_start: 0.9467 (mmm) cc_final: 0.9101 (mmp) REVERT: F 69 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8889 (mp0) REVERT: G 149 LEU cc_start: 0.6099 (mt) cc_final: 0.5394 (pp) REVERT: G 163 LEU cc_start: 0.7134 (tt) cc_final: 0.6613 (mp) REVERT: H 39 MET cc_start: 0.7881 (mmm) cc_final: 0.7527 (mmm) REVERT: H 121 MET cc_start: 0.9050 (ttp) cc_final: 0.7412 (tmm) REVERT: I 4 MET cc_start: 0.8610 (ppp) cc_final: 0.8183 (ppp) REVERT: I 75 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7651 (tpp80) REVERT: J 29 TYR cc_start: 0.8680 (m-80) cc_final: 0.8443 (m-80) REVERT: K 48 MET cc_start: 0.8893 (mmm) cc_final: 0.8605 (mmm) REVERT: L 15 CYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8407 (p) REVERT: M 21 ILE cc_start: 0.9444 (pt) cc_final: 0.9117 (mm) REVERT: M 325 MET cc_start: 0.8002 (ptt) cc_final: 0.7319 (ptt) REVERT: M 416 MET cc_start: 0.8842 (ttp) cc_final: 0.8490 (tpp) REVERT: M 486 MET cc_start: 0.8690 (mpp) cc_final: 0.8341 (mpp) REVERT: M 608 MET cc_start: 0.8159 (tpp) cc_final: 0.7901 (tpp) REVERT: M 617 MET cc_start: 0.8904 (tpt) cc_final: 0.8518 (tpt) REVERT: M 648 MET cc_start: 0.9284 (tmm) cc_final: 0.8796 (ppp) REVERT: M 880 MET cc_start: 0.9113 (mtm) cc_final: 0.8889 (mpp) REVERT: M 929 GLU cc_start: 0.8611 (tp30) cc_final: 0.7864 (tp30) REVERT: M 1063 MET cc_start: 0.9387 (mmm) cc_final: 0.9043 (mmm) outliers start: 29 outliers final: 25 residues processed: 208 average time/residue: 0.2043 time to fit residues: 73.0737 Evaluate side-chains 212 residues out of total 4053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 29 CYS Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 849 MET Chi-restraints excluded: chain M residue 1005 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 408 optimal weight: 0.0010 chunk 92 optimal weight: 0.0470 chunk 249 optimal weight: 0.0980 chunk 204 optimal weight: 10.0000 chunk 387 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 300 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.057740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.041193 restraints weight = 220669.096| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.74 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36406 Z= 0.090 Angle : 0.538 15.627 49646 Z= 0.260 Chirality : 0.039 0.189 5767 Planarity : 0.003 0.045 6108 Dihedral : 12.743 171.414 5678 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.73 % Allowed : 9.80 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.13), residues: 4502 helix: 2.15 (0.14), residues: 1525 sheet: 0.12 (0.19), residues: 741 loop : -0.99 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 28 TYR 0.017 0.001 TYR K 87 PHE 0.038 0.001 PHE M 649 TRP 0.018 0.001 TRP B 229 HIS 0.005 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00194 (36371) covalent geometry : angle 0.52943 (49606) hydrogen bonds : bond 0.02535 ( 1435) hydrogen bonds : angle 3.89207 ( 4163) metal coordination : bond 0.00360 ( 35) metal coordination : angle 3.38850 ( 40) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7343.63 seconds wall clock time: 126 minutes 29.76 seconds (7589.76 seconds total)